I think you'll need to write a script because you want more than just standard alignment. Take a look at obfit.cpp or other alignment scripts and then you can delete the atoms not in the match.
-Geoff > My ultimate goal is to take molecule A, align it to molecule B and then > "delete" all atoms from molecule B and molecule A which are not present in > each other. These aligned atoms of molecule B, will then be compared with the > atoms from Molecule A and their differences in electronegativity will be > calculated for the Molecules. > … > > The input Smart Pattern is the MCS generated but the aligned.sdf contains the > same atoms as Molecule B (atoms which aren't in common aren't removed). >
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